Remove taxonomy in the fasta format of silva database, related to #8

lentendu · Jun 9, 2018 · 9cc2a2d · 9cc2a2d
1 parent 4e6e306
commit 9cc2a2d
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/auxiliary_scripts/update_silva.sh b/auxiliary_scripts/update_silva.sh
@@ -47,7 +47,7 @@ then
 fi
 
 # mothur format
-awk '{print $1}' silva_${VERSION}_SSURef_Nr99_UTAX.fasta > silva_${VERSION}_SSURef_Nr99.fasta
+awk 'BEGIN{FS=";"}{print $1}' silva_${VERSION}_SSURef_Nr99_UTAX.fasta > silva_${VERSION}_SSURef_Nr99.fasta
 awk '$0~"^>"{sub("^>","");gsub("\\|",";");print $1"\t"$2";"}' silva_${VERSION}_SSURef_Nr99_UTAX.fasta > silva_${VERSION}_SSURef_Nr99.taxonomy
 awk '{print $1}' SILVA_${VERSION}_SSURef_Nr99_tax_silva_full_align_trunc.fasta | sed '/>/!s/U/T/g' > silva_${VERSION}_SSURef_Nr99.align.fasta
 cat << EOF > ${TARGET_DIRECTORY}/silva_${VERSION}.txt